Biochemistry

Question 1

A single-stranded DNA oligonucleotide composed of which of the following would move most slowly down an alkaline agarose gel during electrophoresis?

Answer 1

Deoxyguanosine monophosphate

This will be the largest

Question 2

Based on the hypothesized localization of DSO proteins, the region of the plasma membrane that surrounds DSO is most likely rich in which of the following molecules relative to other plasma membrane regions?

A) sterols
B) phospholipids
C) prostaglandins
D) triglycerides

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Answer 2

A) sterols

To maintain a more ordered state, lipid rafts tend to be rich in sterols (cholesterols in animals, phytosterols in plants) and relatively poor in phospholipids comapred to other regions of the membrane

The passage states that DSO is hypothesized to be localized to lipid rafts. Therefore, DSO is most likely in an environment that is rich in cholesterol compared to other regions of the plasma membrane

Question 3

Functional group common in wax

Answer 3

esters

Question 4

Which parameter would NOT be affected by the addition of phosphoglycerate mutase?

A) the stability of the transition state between 3-phosphoglycerate and 2-phosphoglycerate
B) the equilibrium concentrations of 3-phosphoglycerate and 2-phosphoglycerate
C) the activation energy barrier between 3-phosphoglycerate and 2-phosphoglycerate
D) The rate constant for conversion of 3-phosphoglycerate and 2-phosphoglycerate

Answer 4

B) the equilibrium concentrations of 3-phosphoglycerate and 2-phosphoglycerate

Question 5

An enzyme kinetics assay reveals that Vmax = 100 nmols/s and Km . 10 um. For this assay, what substrate concentration is required for a reaction rate V0 of 75 nmol/s?

Answer 5

30 uM

Vo=V + [S] / Km + [S)
Michaelis-Menten equation

Question 6

The reaction shown in Figure 2 is most likely immediately followed by a reaction catalyzed by which type of enzyme?

A) endonuclease
B) exonuclease
C) ligase
D) polymerase

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(reaction is DNA repair)

Answer 6

A) endonuclease

Figure 2 shows removal of the uracil base from a DNA strand by UDG but does not show cleavage of the DNA backbone. Before a ligase can insert a new base, the relevant section of the DNA backbone must be removed. Therefore, of the choices given, an endonuclase is most likely to catalyze the reaction immediately after removal of the uracil base.

Question 7

Suppose that just prior to replication in a cell, an adenine residue at a particular position in a DNA strand is converted to hypoxanthine, and this mistake is corrected only after replication. After the correction, the cell divides. Based on the correction, the cell divides. Based on the most probably DNA base pairing pattern of hypoxanthine, which of the following mutations would most likely be found at the same position in the DNA of one of the daughter cells?

A) A mutation in which the adenine is replaced by cytosine and its complementary thymine is replaced by guanine
B) A mutation in which the adenine is replaced by guanine and its complementary thymine is replaced by cytosine
C) A mutation in which the adenine is replaced by thymine and the complementary thymine is replaced by adenine
D) A mutation in which the adedine remains adenine and the complementary thymine is replaced by cytosine

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Answer 7

B) A mutation in which the adenine is replaced by guanine and its complementary thymine is replaced by cytosine

Figure 1 shows the structures of several modified nucleotides, including hypoxanthine. As a derivative of adenine, hypxanthine is a purine, so it pairs best with a pyrimidine.

The hydrogen bond acceptor in hypoxanthine (C=O) must pair with a donor, and the donor (N-H) must pair with an acceptor. Of the two standard DNA pyrimidines, only cytosine has a configuration that can satisfy these hydrogen bonding requirements.

Because hypoxanthine would most likely base pair with cytosine during replication, the thymine that is normally paired with adenine would be replaced by cytosine. When the hypoxanthine is subsequently corrected, it will be replaced by guanine to maintain pairing with the cytosine. When the cell divides, this DNA will be passed to one of the daughter cells. Therefore, the daughter cell will most likely contain a mutation in which the adenine was replaced by guanine and its complementary thymine was replaced by cytosine.

Question 8

Both isoforms of destabilase have approximately the same kcat values for isopeptidase activity at optimal pH, but Figure 1 shows that when 5uL of each purified enzyme was provided with saturating levels of substrate, the isoforms had different levels of activity. What factor could explain this apparent discrepency?

A) Isoform 2 had less activity than isoform 1 because isoform 2 did not operate at Vmax under saturating conditions
B) The 5uL sample of isoform 1 had a higher enzyme concentration than the isoform 2 sample because the affinity column bound isoform 1 more tightly ‘
C) Isoform 1 had less activity than isoform 2 because isoform 1 became denatured at pH 6
D) the 5 uL sample of isoform 2 had a higher enzyme concentration than the isoform 1 sample because E. coli expressed isoform 2 at higher levels

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Answer 8

D) the 5 uL sample of isoform 2 had a higher enzyme concentration than the isoform 1 sample because E. coli expressed isoform 2 at higher levels

Vmax = kcat x [E]
Therefore, enzymes at a higher concentration have a higher Vmax

The passage thats that isoforms 1 and 2 have approximately the same kcat values for both isopeptidase and glycosidase activities at optimal pH, yet figure 1 shows that 5 uL of isoform 2 has substantially higher activity than the same volume of isoform 1

The fact that equal volumes of each enzyme were used does not necessarily mean that both 5 uL samples had the same concentration after purification.

Question 9

What conclusion is least supported by the data in Figure 2?

A) Glutamate at position 14 is required for glycosidase activity but not for isopeptidase activity
B) Mutating serine at position 31 has no effect on isopeptidase activity or glycosidase activity
C) Lysine at position 28 is required for isopeptidase activity but not for glycosidase activity
D) Mutating histidine at position 92 has the smallest impact of the tested mutations on glycosidase activity

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Answer 9

B) Mutating serine at position 31 has no effect on isopeptidase activity or glycosidase activity

Figure 2 shows the effects of several mutations on both isopeptidase and glycosidase activities in isoform 2 of the destabilase enzyme and expresses them as a percentage of the activity observed in the wild-type enzymes

• When glutamate at position 14 is mutated to alanine (E14), isopeptidase activity remains high but glycosidase activity is essentially zero, therefore, figure 2 strongly supports the conclusion that high glutamate residue is required for glycosidase activity but not for isopeptidase activity (Choice A)
• When lysine at position 38 is mutated to alanine (K38A), isopeptidase activity is essentially zero, whereas glycosidase activity is only slightly diminished. Therefore, figure 2 strongly supports the conclusion that this lysine residue is required for isopeptidase activity but not for glycosidase activity
• When histidine at position 92 is mutated to alanine (H92A), glycosidase activity remains near 100% of wild-type levels and is higher than the glycosidase activity of any other mutation tested. Therefore, mutating this histidine residues does have the smallest impact of all the tested mutations on glycosidase activity (Choice D)

Question 10

Dephosphorylation of pRCAN1 by calcineurin most likely causes which of the following?

A) INcreased calcineurin activity
B) Upregulation of GPCR activity
C) Decreased p38a activity
D) Downregulation of T-cell activation

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Answer 10

D) Downregulation of T-cell activation

Feedback inhibition

The passage states that pRCAN1 can be dephosphorylated by calcineurin, which yields RCAN1. RCAN1 (the product) can then inhibit calcineurin.

The passage also thats that:

1. organ transplants are more successful when immune responses are suppressed
2. calcineurin activates T cells by dephosphorylating NFAT, and
3. calcineurin inhibitors are commonly used in combination with organ transplant procedures

These statements indicate that calcineurin inhibitation helps suppress the immune response by decreasing T-cell activation. Dephosphorylation of pRCAN1 would most likely lead to inhibition of calineurin by producing the inhibitor RCAN1. This would result in inability to dephosphorylate NFAT, which would lead to downregulation of T-cell activation

Question 11

Competitive inhibitors bind

Answer 11

E only

Question 12

Umcompetitive inhibitiors bind

Answer 12

ES only

Question 13

Mixed inhibitors bind

Answer 13

both E and ES, though they may have a higher affinity for E than for ES, or vice versa

Question 14

Noncompetitive inhibitors

Answer 14

are a special case of mixed inhibitor in which the affinities for E and ES are exactly equal

Question 15

Based on the predicted structure of a certain gene product, the corresponding gene is believed to encode a glycolsylfertransferase that post-translationally modifies substrate proteins as shown in the diagram:

Which of the following experiments would best test this prediction?

A) Flourescently label the proposed glycosyltransferase, mix it with the subtrate protein and donor molecule, then assess whether the proposed glycosyltransferase is retained on a column that binds the carbohydrate
B) Mix the substrate protein and donor molecule, with or without the proposed glycolsyltrasnferase, then perform a Western blot using an antibody specific to the substrate protein
C) incubate the donor molecule and substrate protein, with or without the glycolsyltransferase, then use mass spectrometry to measure the mass of the donor molecule
D) Add a tritium label to the carbohydrate, incubate the donor molecule and substrate protein with or without the proposed glycosyltransferase, then measure tritium levels in the purified substrate protein

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Answer 15

D) Add a tritium label to the carbohydrate, incubate the donor molecule and substrate protein with or without the proposed glycosyltransferase, then measure tritium levels in the purified substrate protein

Transferases are a class of enzymes that move a chemical group from one molecule to another. For example, glycosyltransferases move carbohydrate (glycosyl) groups. To confirm that a given enzyme is a glycosyltransferase, the movement of the carbohydrate group from one molecule to another must be observed to a much greater degree in the presence of the enzyme than in its absence.

Chemical groups are commonly tracked by replacing one type of atom in the group with a radioactive isotope of that atom. Tritium is a radioactive isotope of hydrogen that is often used to track organic chemical groups.

Question 16

Oxidoreductases

Answer 16

Oxidation-Reduction

A- + B –> A + B-

Question 17

Transferases

Answer 17

Functional group transfer

A-B + C –> A + B-C

Question 18

Hydrolases

Answer 18

Hydrolytic cleavage of a molecule into two molecules

A-B + H2O –> A-H + B-OH

Question 19

Lyases

Answer 19

Group removal or additional with electron rearrangement to form double bonds
X-Y
| |
A B –> A=B + X-Y

Question 20

Isomerases

Answer 20

Functional group movement within a molecule
X Y –> Y X
| | –> | |
A—B –> A—B

Question 21

Ligases

Answer 21

Joining two molecules to form one via bond formation and ATP hydrolysis
ATP + A + B –> A-B + ADP + Pi

Question 22

The electron transport chain results in the generation of:

Answer 22

a proton concentration gradient across the inner mitochondrial membrane, which drives phosphorylation of ADP

Question 23

Enzyme A catalyzes the conversion of substrate S to product P. When enzyme A is phosphorylated, its kcat value changes from 10 s^-1 to 5s_1, and its Km value changes from 100 uM to 20 uM. If equal concentrations of each enzyme form are used then compared to the unphosphorylated enzyme A, the phosphorylated form:

A) has a higher catalytic efficiency and yields a faster reaction rate when [S] < 2um
B) has a higher turnover number and yields a faster reaction rate under saturating conditions
C) has a lower affinity for S and yields a slower reaction rate at all [S]
D) is allosterically inhibitied and yields a lower reaction rate at all [S}

Answer 23

A) has a higher catalytic efficiency and yields a faster reaction rate when [S] < 2um

Catalytic efficiency is a mreasure of how quickly an enzyme catalyzes a reaction at low substrate concentrations (eg, [S] < Km). An enzyme is efficient if a small amount of substrate yields a high reaction rate V0. Catalytic efficiency = Kcat / Km. A higher kcat and/or lower Km contributes to a higher catalytic effiency, and therefore to a faster reaction rate at low substrate concentrations relative to less-efficient enzymes.

The question indicates that enzyme A undergoes a decrease in both kcat and Km upon phosphorylation. However, Km decreases by a greater factor than kcat, so the kcat/kM ratio increases. Therefore, the phosphorylated form has a higher catalytic efficiency than the low unphosphorylated form, and the phosphorylated form yields a faster reaction rate at low concentrations (eg, below 20 um)

Question 24

Nucleotides can combine to form long chains known as polynucleotides or nucleic acids (ie, RNA or DNA) as catalyzed by RNA polymerase or DNA polymerase. In biological systems, lengthening of these chains occurs

Answer 24

from the 5’ end to the 3’ end (ie, new nucleotides are added to the 3’ end of the chain). During this process, the 3’ hydroxyl group of the growing chain acts as a nucleophile to attack the 4’ a-phosphate of the incoming nucleotide

Question 25

After cardiac cells depolarize under physiologically normal conditions, extracellular Na+ enters the cells via a specific plasma membrane. The Na+ transport provides the energy needed to pump intracellular Ca2+ to the extracellular space. This Na+/Ca2+ exchange depends on a preceding increase in intracellular [Ca2+] in reponse to the cell’s decreased electric potential. This preceding increase in Ca2+ is most likely evidence of:

A) direct voltage-dependent activation of the exchanger
B) entry of Ca2+ ions into the intracellular fluid through a voltage-dependent membrane channel
C) activation of a ligand-gated Ca2+ channel
D) transport of Ca2+ ions against their concentration gradient through a voltage-gated membrane channel

Answer 25

B) entry of Ca2+ ions into the intracellular fluid through a voltage-dependent membrane channel

Voltage gated ion channels: Depolarization triggers shape change, opening voltage-gated Ca2+ channel
Before depolarization, the voltage-gated Ca2+ channel is closed –> after depolarization, increased [Ca2+] activates exchange of Na+ and Ca2+

Not choice D because: the question indicates that Ca2+ transport from intracellular to extracellular space requires energy input; therefore, Na+/Ca2+ exchange involves transport against the calcium gradient. However, the voltage-gated channel facilitates Ca2+ entry into the cell, which must occur DOWN the gradient

Question 26

If a frameshift mutation changes the number of amino acids in a protein from 591 to 626, the difference between molecular weights of the wild-type and mutant proteins would be closest to:

Answer 26

4 kDA

Wildtype protein: 591 Amino Acids x 110 Da/AA = 65 kDA

Elongated mutant protein: 626 AA x 110Da/AA = 69 kDA

69-65 = 4

Question 27

In Fischer projectsions, cyclic D-sugars with a hydroxyl group to the right of the anomeric carbon in the

Answer 27

a-conformation

Question 28

Reducing sugars

Answer 28

contain free anomeric carbons that provide reducing power when they are oxidized. In linear form the anomeric carbon is an aldehyde or a ketone, and incyclic form reducing sugars have hemiacetal or hemiketal configurations. Nonreducing sugars contain acetal or ketal structures in their cyclic forms

Question 29

Lower melting point

Answer 29

• Faster denaturation rates
• Less stable 3D structure
• Weaker or fewer intermolecular forces

Question 30

the absence of which of the following lipids is most likely to affect the assembly of viral envelopes?

A) palmitic acid
B) triacylglyveridse
C) sphingomyelin
D) phosphatidylserine

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Answer 30

D) phosphatidylserine

Influenza A obtains its viral envelope from the plasma membrane of its host cell. However, the passage states that the composition of the envelope differs significantly from the plasma membrane. Unlike human membranes, the viral envelope contais mostly phosphatidylethanoalime and negatively charged glycerophosphplipids.

of the choices presented, phosphatidylserine is the only negatively charged glycerophospholipid. Therefore, its absence is most likely to affect the assembly of the viral envelope.

Question 31

Which of the following correctly describes the stereospecific formation of a citric acid cycle intermediate?

A) citrate synthase consumes ATP to generate citrate from oxaloacetate and actyl-coA
B) fumarase converts furmate into both l and d malate through a condensation reaction
C) succinyl coA synthetase consumes GTP to transform succinyl coA to succinate
D) Aconitase converts citrate into isocitrate through an intermediate

Answer 31

D) Aconitase converts citrate into isocitrate through an intermediate

The first reaction in the cycle is the conversion of citrate to isocitrate by the aconitase enzyme through an intermediate called cis-aconitase. Aconitase catalyzes consecutive dehydration and hydration reactions that exchange the hydrogen atom and hydroxyl group of the second and third carbon. This isomerase activity results in the transformation of citrate, which is achiral, intro isocitrate, which contains two new chiral centers

Question 32

Which best describes the action of PH on AMPK activity?

A) PH stimulates leptin action on the nervous system
B) PH antogonizes direct leptin action on muscles
C) PH antagonizes leptin action on the nervous system
D) PH stimulates direct leptin action on muscles

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Answer 32

C) PH antagonizes leptin action on the nervous system

According to the passage, leptin stimulates AMPL activity by activate the sympathetic nervous system, and it can also be directly on skeletal muscles. Intrahypothalamic injections allow leptin to be administered directly to the CNS, but muscles are not directly affected in this scenario

Question 33

The addition of AMPK phosphatases to skeletal muscles exposed to leptin would result in which of the following?

A) increasing shuttling of fatty acids from the cytosol into the mitochondria
B) Increased funneling of electrons to carriers NAD+ and FAD
C) Upregulated activity of the acyl carrier protein in fatty acid synthesis
D) Upregulated phosphorylation of acetyl-coA carboxylase

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Answer 33

C) Upregulated activity of the acyl carrier protein in fatty acid synthesis

The passage states that phosphorylation activates AMPK; in this scenario, AMPK phosphatases in leptin-exposed muscles would dephosphorylate AMPL and thereby inactivate it. Inactive AMPK would then be unable to phosphorylate and inhibit ACC (D). Without inhibition, ACC will then carry out the first and rate limiting step of fatty acid synthesis by carboxylating acetyl CoA to malonyl coA, promoting fatty acid synthesis and preventing b-oxidation

Because ACC activity is unhibitied in the presence of AMPK phosphates, fatty acid synthesis is stimulated and the activity of the acyl carrier protein is increased

Question 34

Which of the following most accurately describes the interaction between the antibody a-Flag and its target, Flag-IRS4?

A) A covalent protein-protein interaction
B) A noncovalent protein-protein interaction
C) A covlanet protein carbohydrate interaction
D) A noncovalent protein carbohydrate interaction

Answer 34

B) A noncovalent protein-protein interaction

Because both the antibody (a-Flag) and its target (Flag-IRS4) are proteins, the interaction between them is a protein-protein interaction. Because antibodies generally bind their targets noncovalently, this interaction can be classified more specifically as a noncovalent protein interaction

Question 35

Based on the given sequences of the two peptide tags, which of the following characteristics do the Flag and myc peptides have in common: They have the same

A) Number of nonpolar residues
B) binding interactions with a-Flag
C) number of acidic residues
D) net charge at physiological pH

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Flag = DYKDDDDK 
myc = EQKLISEEDL

Answer 35

D) net charge at physiological pH

Flag = DYKDDDDK
D= -1 (x5)
K = +1 (x2)
Net charge: -3

Myc = EQKLISEEDL 
E =-1 (x4) 
K = +1 
Q,L,I,S = 0 
Net charge: -3 

Not B, antibodies are highly specific typically bind a single chemical group called an epitope.

Question 36

To conclude that IRS4 binds ASb-4, wahat assumption must be made about the recombinant proteins?

A) Recombinant Flag-IRS4 and myc-ASb-4 are expressed at similar levels
B) HEK293 cells do not express IRS4 and ASb-4 endogenously
C) Flag and myc are not involved in interactions between Flag-IRS4 and myc-ASb-4
D) Flag-IRS4 and myc-ASb-4 are tagged at their N-termini only

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Answer 36

C) Flag and myc are not involved in interactions between Flag-IRS4 and myc-ASb-4

The biological function of a protein is determined by the sequence of amino acids that make up that protein (primary structure). Altering the sequence of a protein may alter its function.

Question 37

Which of the following is the most likely mechanism by which the sb region of ASb-4 decreases IRS4 levels?

A) the sb domain facilitates ubiqutionation of IRS4, targeting it to the proteasome
B) the sb domain induces IRS4 expression by entering the nucleus to bind DNA
C) the sb domain prevents degredation of IRS4 by inhibiting proteases
D) the sb domain becomes ubiqutinated, causes IRS4 to enter to lysosome

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Answer 37

A) the sb domain facilitates ubiqutionation of IRS4, targeting it to the proteasome

Figure 2 shows that when myc-Asb-4 is present, a ubiqutin tag is detected. the figure also shows that ubiqutin binds to IRS4 only when the sb domain of myc-Asb-4 is present. Therefore, myc-Asb-4 likely causes ubiquitination of Flag-IRS4. Ubiquitin is not detected when the sb domain is removed, indicating that this domain is required for ubiquitination. Proteins with ubiquitin tags are typically targeted to the proteasome for destruction.

Question 38

Catalytic efficiency

Answer 38

(Vmax/[E]) / Km

Question 39

Researchers isolate a protein that runs as a single band on a nonreducing SDS-PAGE gel but as two distinct bands on a reducing gel. The protein is most likely a

A) heteromultimer that formed in the oxidizing environment of the endoplasmic reticulum
B) heteromultimer that formed in the reducing environment of the cytosol
C) homomultimer that formed in the oxidizing environment of the endoplasmic reticulum
D) homomultimer that formed in the reducing environment of the cytosol

Answer 39

A) heteromultimer that formed in the oxidizing environment of the endoplasmic reticulum

The formation of two distinct bands when the multimer is broken suggests that the protein contained nonidentical subunits, making it a heteromultimer.

The fact that a reducing gel is required to break the multimer indicates that disulfide bonds are present. They most likely formed in the oxidizing environment of the endoplasmic reticulum

In reducing environments such as the cytosol, proteins are unlikely to form disulfide bonds. Therefore, such proteins are unlikely to be affected by a reducing gel, as they are already reduced

Question 40

Which of the following could researchers add to restore oxygen consumption in the presence of drug X?

A) cyt Cred
B) cyt Cox
C) ubiqinol
D) ubiquinone

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Answer 40

A) cyt Cred

Oxygen consumption in the ETC takes place in complex IV< where O2 gets reduced to become water. The electrons needed to reduce oxygen are provided by reduced cytochrome c, which is converted to its oxidized form in the reaction catalyzed by complex IV.

Figure 1 shows that cyt red is depleted in the rpesence of drug X. Because cyt c red is required for complex IV to function, cyt red depletion eventuallu results in decreased complex IV activity and therefore decreased oxygen consumption. To restore normal oxygen consumption levels, more cyt cred is needed.

Question 41

Based on the information in the passage, FCCP most likely causes a decrease in energy production by

A) decoupling the movement of protons down their concentration gradient from ATP synthase
B) carrying more protons into the intermembrane space than are pumped by the ETC alone
C) shifting the proton gradient further away from equilibrium than is achieved by the ETC alone
D) causing a decrease in ETC activity, resulting in fewer available protons for ATP synthase

Answer 41

A) decoupling the movement of protons down their concentration gradient from ATP synthase

ATP synthesis is driven by protons crossing the inner mitochondiral membrane through ATP synthase. When protons are transported across the membrane by means that bypass ATP synthase, the energy released in the process cannot be used to produce ATP. This phenomenon is known as “decoupling” because proton transfer is no longer coupled to ATP synthesis